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- PDB-6i93: R2-like ligand-binding oxidase G68L mutant with aerobically recon... -

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Basic information

Entry
Database: PDB / ID: 6i93
TitleR2-like ligand-binding oxidase G68L mutant with aerobically reconstituted Fe/Fe cofactor
ComponentsRibonucleotide reductase small subunit
KeywordsOXIDOREDUCTASE / R2-LIKE LIGAND-BINDING OXIDASE / MN/FE COFACTOR / RIBONUCLEOTIDE REDUCTASE R2 SUBUNIT FOLD / METALLOPROTEIN OXIDOREDUCTASE
Function / homology
Function and homology information


deoxyribonucleotide biosynthetic process / oxidoreductase activity / metal ion binding
Similarity search - Function
R2-like ligand binding oxidase / Ribonucleotide reductase small subunit family / Ribonucleotide reductase, small chain / Ribonucleotide Reductase, subunit A / Ribonucleotide Reductase, subunit A / Ribonucleotide reductase-like / Ferritin-like superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
: / OCTANOIC ACID (CAPRYLIC ACID) / R2-like ligand binding oxidase
Similarity search - Component
Biological speciesGeobacillus kaustophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.101 Å
AuthorsGriese, J.J. / Hogbom, M.
CitationJournal: J.Biol.Chem. / Year: 2019
Title: Chemical flexibility of heterobimetallic Mn/Fe cofactors: R2lox and R2c proteins.
Authors: Kutin, Y. / Kositzki, R. / Branca, R.M.M. / Srinivas, V. / Lundin, D. / Haumann, M. / Hogbom, M. / Cox, N. / Griese, J.J.
History
DepositionNov 22, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 16, 2019Provider: repository / Type: Initial release
Revision 1.1Oct 23, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_PubMed / _citation.title ..._citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Dec 11, 2019Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.3Jan 24, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Ribonucleotide reductase small subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,2754
Polymers37,0191
Non-polymers2563
Water1,54986
1
A: Ribonucleotide reductase small subunit
hetero molecules

A: Ribonucleotide reductase small subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,5508
Polymers74,0382
Non-polymers5126
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
Buried area6990 Å2
ΔGint-70 kcal/mol
Surface area20870 Å2
MethodPISA
Unit cell
Length a, b, c (Å)55.889, 96.892, 128.429
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222
Components on special symmetry positions
IDModelComponents
11A-508-

HOH

21A-569-

HOH

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Components

#1: Protein Ribonucleotide reductase small subunit


Mass: 37018.910 Da / Num. of mol.: 1 / Mutation: G68L
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Geobacillus kaustophilus (strain HTA426) (bacteria)
Strain: HTA426 / Gene: GK2771 / Plasmid: pET-46 Ek/LIC / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: Q5KW80, ribonucleoside-diphosphate reductase
#2: Chemical ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe
#3: Chemical ChemComp-OCA / OCTANOIC ACID (CAPRYLIC ACID)


Mass: 144.211 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H16O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 86 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.35 Å3/Da / Density % sol: 47.62 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 27.5% (W/V) PEG 1500, 0.1 M HEPES-NA PH 7.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: MAX II / Beamline: I911-3 / Wavelength: 1 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: May 10, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.1→50 Å / Num. obs: 20702 / % possible obs: 99.7 % / Observed criterion σ(I): -3 / Redundancy: 4.1 % / Biso Wilson estimate: 36.6 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.059 / Rrim(I) all: 0.068 / Net I/σ(I): 17.98
Reflection shellResolution: 2.1→2.23 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.87 / Mean I/σ(I) obs: 1.63 / Num. unique obs: 3264 / CC1/2: 0.613 / Rrim(I) all: 1.002 / % possible all: 99

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
XDSdata reduction
XDSdata scaling
PHENIXphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 4HR0

4hr0


Resolution: 2.101→27.964 Å / SU ML: 0.25 / Cross valid method: FREE R-VALUE / σ(F): 2 / Phase error: 21.93
RfactorNum. reflection% reflectionSelection details
Rfree0.2222 1036 5 %random selection
Rwork0.1697 ---
obs0.1724 20702 99.73 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.101→27.964 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2361 0 12 86 2459
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0172450
X-RAY DIFFRACTIONf_angle_d1.1123294
X-RAY DIFFRACTIONf_dihedral_angle_d16.4251448
X-RAY DIFFRACTIONf_chiral_restr0.057346
X-RAY DIFFRACTIONf_plane_restr0.008425
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.101-2.21170.30691430.26542727X-RAY DIFFRACTION99
2.2117-2.35020.24591470.21722772X-RAY DIFFRACTION100
2.3502-2.53150.23291470.19112789X-RAY DIFFRACTION100
2.5315-2.78610.24951460.17932799X-RAY DIFFRACTION100
2.7861-3.18880.2071470.17162788X-RAY DIFFRACTION100
3.1888-4.01560.21651510.15622844X-RAY DIFFRACTION100
4.0156-27.96630.20631550.14972947X-RAY DIFFRACTION100

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